spacer
Collapse General Courses Information
spacer
EBITrainingOnsite CoursesJalview Course

EBI Affiliated Course - Multiple Sequence Alignment and Analysis with Jalview

Course Summary

Title: Multiple Sequence Alignment and Analysis with Jalview
Date: 1-2 December 2011
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organiser: Geoff Barton, Jim Procter
Admin Support: Johanna Langrish
Registration Deadline: 18 November 2011 - 12:00 midday (GMT)



Course Overview

This course spans the basic, intermediate and advanced functions of the Jalview sequence alignment, visualisation, annotation, and analysis system. The course begins with an evening reception dinner and introductory talk on the evening of the 1st December at the Red Lion, Whittlesford, and continues the following day in the EMBL-EBI training facility with a series of hands-on sessions where you will be able to try out different Jalview capabilities. There will also be the opportunity for participants to work with their own data, and discuss analysis problems with the Jalview team.

Is it right for me?

This course is suitable for anyone who needs to create, manipulate, annotate and publish nucleotide or protein sequence alignments, and use them to explore biological function. There will be introductory material for people with little or no experience in biological sequence analysis, but the course is also an opportunity for people with more extensive bioinformatics knowledge to gain a deeper understanding of Jalview.

Programme

 

Time Topic
Day 1 - Thursday 1 December 2011 @ The Red Lion Hotel, Whittlesford, UK (next to the Holiday Inn Express Hotel)
19:00 Welcome dinner and introductory talk from Prof. Geoff Barton
Day 2 - Friday 2 December2011 @ EMBL-EBI IT Training Room, WTGC, Hinxton, UK
08:15 Shuttle bus from Holiday Inn Express, Duxford (Whittlesford) to EBI (for resident delegates only)
08:30 Refreshments and registration
09:00 Session 1 : Introduction to Jalview
  • Getting started
    • loading and saving alignments
    • navigation and editing
    • colouring and groups
    • formatting and figure generation
  • DNA, Protein and Jalview
    • Working with PDB structures
    • DNA coding regions and Protein products
    • working with sequence annotation
10:30 Refreshments
11:00 Session 2: Alignment, annotation and analysis
  • Creating your own alignments
    • Downloading and Installing JABA
    • Configuring Jalview for local alignment
  • Phylogenetic trees and principal component analysis
  • Alignment annotation
    • Subfamily analysis
    • Protein secondary structure prediction
12:30 Lunch
13:30 Session 2 continues
14:00 Session 3: Advanced Jalview and Jalview Clinic
  • Overview of advanced topics
    • Batch processing with the Jalview command line
    • Putting your alignments on the web with JalviewLite
    • Scripting with Jalview and Groovy
14:30 Jalview Clinic / Advanced topic exercises
15:00 Refreshments
15:30 Jalview Clinic / Advanced topic exercises continues
16:20 Closing remarks
16:30 Departure

Registration

There will be a maximum of 35 participants on this course, registration is on a first come first serve basis. Registration closes 18 November 2011 - 12:00 midday (GMT).

Registration Fees:
1. Evening reception & full day tutorial (No Accommodation) = £45.00
2. Evening reception, accommodation & full day tutorial = £57.00

Please note that the registration fees includes:

1. Evening reception & full day tutorial (No Accommodation) = £45.00

  • All meals (dinner, lunch and refreshment breaks)
  • Course materials
  • Use of EBI IT Training Room computer during the course

2. Evening reception, accommodation & full day tutorial = £57.00

  • All meals (dinner, breakfast, lunch and refreshment breaks)
  • Accommodation for 1 night (check in 1 December 2011, check out 2 December 2011), in the Holiday Inn Express, Duxford (http://www.hiexpresscambridgeduxford.co.uk/)
  • Transport from the accommodation to the EBI on Friday 2 December 2011
  • Course materials
  • Use of EBI IT Training Room computer during the course
NOTE: All delegates will need to arrange their own travel to and from the course.

You will need to pay by credit card as you submit your registration - therefore please have your card to hand. To register for this workshop please use the following link:

Registration> > > >

Items marked * are mandatory. Incomplete registrations will not be processed.

Top

spacer
spacer